> Quoting Miguel <miguel=40jmol.org>:
>
>> It is not clear to me where you want to take this disussion.
>>
> I started this discussion to help us to decide what we should
> use for highlighting boundaries between two amino
> acids: 'pmesh' or 'pseudo atoms + bonds'.
Please be patient with me.
Remember that I am not a chemist and do not understand anything about the=
applications that you are trying to build.
I have no idea what the 'boundary between two amino acids' is.
All I understood was 'can I put a label on a pmesh'?
> With the current state of Jmol we could only use pmesh
> combined with a pseudo atom for labelling. Therefore we
> would most probably use 'pseudo atoms + bonds' although the
> highlighting wouldn't be as good as with 'pmesh'.
I am getting confused.
> Because I don't want to force adding features for 'misusing'
> bonds I didn't went further in that direction.
Good. I do not like to misuse features.
> If pmesh labelling would be added we would presumably
> use 'pmesh', even with a lot of different files.
But this sounds like you would be misusing the pmesh command
> I like Timothy's idea of a new annotation object best, because
> it would make any precomputing and/or changing of the PDB files
> unnecessary.
Tim wrote:
>> it seems to me that it might be simpler to add a new kind of
>> annotation object (like a label, but a filled rectangular cube). i.e.=
,
>>
>> set blocksize 12
>> color blocks red
>> block aa3,aa4
> But I guess it would be more work than adding a lablling
> command for 'pmesh'.
I am in favor of adding features if they are generally useful.
We need to restart this discussion from the beginning.
Draw me a picture of what you want. Use a graphics program or use a penci=
l
& paper and scan the results.
Tim sent me this url:
http://www.expasy.org/cgi-bin/prosite/PSView.cgi?ac=3DPS50020&onebyarch=3D=
1&hscale=3D0.6
But I do not understand how this relates to your request.
Miguel

Quoting Miguel <miguel@...>:
> It is not clear to me where you want to take this disussion.
>
I started this discussion to help us to decide what we should use for
highlighting boundaries between two amino acids: 'pmesh' or 'pseudo atoms +
bonds'. With the current state of Jmol we could only use pmesh combined with a
pseudo atom for labelling. Therefore we would most probably use 'pseudo
atoms +
bonds' although the highlighting wouldn't be as good as with 'pmesh'.
Because I
don't want to force adding features for 'misusing' bonds I didn't went further
in that direction. If pmesh labelling would be added we would presumably use
'pmesh', even with a lot of different files.
I like Timothy's idea of a new annotation object best, because it would
make any
precomputing and/or changing of the PDB files unnecessary. But I guess
it would
be more work than adding a lablling command for 'pmesh'.
Regards,
Rolf
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El 20 Oct 2005 a las 0:31, Timothy Driscoll escribi=F3:
> hi Angel,
>
> just curious: that atom naming system is not familiar to me. is it
> specific to lipids?
Hi, Tim
As far as I know, it's not standard. There are few lipids in the PDB
or in other databases, so I don't think there is a standard
nomenclature.
These PDB files are a lipid bilayer with 200 phospholipid molecules,
obtained through molecular dinamics simulation and geometric
duplication of molecules.
H. Heller, M. Schaefer & K. Schulten [Theoretical Biophysics Group,
Beckmann Institute, University of Illinois, Urbana-Champaign, U.S.A.]
"Molecular dynamics simulation of a bilayer of 200 lipids in the gel
and in the liquid-crystal phases", J. Phys. Chem. 97:8343-60, 1993
http://www.lrz-muenchen.de/~heller/membrane/membrane.html
Links via Protein Explorer:
http://molvis.sdsc.edu/protexpl/pe.htm?id=3D../pdb/cutc2.pdbhttp://molvis.sdsc.edu/protexpl/pe.htm?id=3D../pdb/cutg2.pdbhttp://molvis.sdsc.edu/protexpl/pe.htm?id=3D../pdb/cutf2.pdb
I don't know how the authors decided to label the atoms, but since
it is a manually-made PDB I suspect they simply wanted to assign a
unique, reasonably comprehensible name to each.
I checked against the PDB file format description and it is according
to it, but the use of the first number and its character position is
not frequently used in most models (proteins, nucleic); that's the
reason Jmol gets funny about them.
BTW, I solved the problem using wilcards in the atom selector.
=B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7=
=B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7
Dr. Angel Herraez
Dep. Bioquimica y Biologia Molecular, Universidad de Alcala
E-28871 Alcala de Henares (Madrid), Spain
fax: +34-91 885 45 85

Angel & Miguel wrote:
>
>> Hello all
>> I have a PDB file in which some atoms have 4-character ID starting wit=
h
>> a number; Jmol does not allow me to select them
=5Bsnip=5D
>
> This looks like a fundamental problem with the Jmol atom expression
> parser.
>
> Having the integer first is causing problems.
I have taken a look at this. The problem is worse than I thought.
In the expression
select *.1h47
the '.1' is being recognized by the lexical parser as a floating point
number.
That means that this problem is more complicated than I expected. I do no=
t
see an easy solution. I fear that it will require rethinking/rewriting th=
e
expression parser. That will not happen in the near future.
Miguel
-----
Open Source Molecular Visualization
http://www.jmol.org
miguel=40jmol.org
-----

> On 17 Aug 2005 at 8:59, Miguel
> announced Jmol prerelease 10.00.32
>
>> - default center of rotation is now the center of the bounding box
>> instead of the average point
>> - centerAt provides additional flexibility for defining the center of=
>> rotation
>
> This =22centerAt=22 is not documented. Can anyone explain it?
> I am interested since I have had trouble with positioning some models.
centerAt absolute=7Cboundbox=7Caverage =7B <x> <y> <z> =7D
absolute specifies absolute angstroms coordinates
boundbox is relative to the center of the boundbox. The boundbox is
defined by the minimum and maximum atom center coordinates along each of
the cartesian axes.
average is relative to the average atom position. Also known as the
'unweighted center of gravity'
If coordinate values are not specified then they are assumed to be 0,0,0
=23 absolute cartesian coordinates 1.0, 2.0, 3.0
centerAt absolute 1.0 2.0 3.0;
=23 the following two are equivalent
centerAt absolute;
centerAt absolute 0 0 0;
=23 offset relative to the center of the boundbox
centerAt boundbox 10 20 -30
=23the following are equivalent to the Chime + new default centering posi=
tion
centerAt boundbox 0 0 0;
centerAt boundbox;
center;
center all;
center *;
select all; center selected;
=23 offset relative to the average atom position
=23 this was the default in Jmol 10.00
centerAt average 1 1 1;
=23 the following are equivalent
centerAt average 0 0 0;
centerAt average;
Miguel